Motors acting up

I have several motors powering the same drivetrain on a flywheel design. When we were testing/assembling etc. the whole thing worked fine. It is a very simple construction with 6 gears being powered by seperate motors that alternate turning clockwise and anti-clockwise down the line:

  ___    ___    ___    ___    ___    ___  
 |   |  |   |  |   |  |   |  |   |  |   | 
 |___|  |___|  |___|  |___|  |___|  |___| 
   «      »      «      »      «      »   
 __|__  __|__  __|__  __|__  __|__  __|__ 
|     ||     ||     ||     ||     ||     |
 —————  —————  —————  —————  —————  —————
 36-tooth gears

This all worked when testing, but when we flipped it upside down and mounted it (because it was easier to test with the motors on the top) and then assembled the rest, the motors stopped working. When we turned it on, all of the motors would work, and the flywheel would start, and then it the motors would start turning against each other and over-heat. The code has been bastardized to just give the motors power, nothing fancy, so that is not the problem. The connections to all the motors were taped up before testing and haven’t been altered since, so that shouldn’t be a problem, and when we checked a bunch they all looked fine. Our cortex has been acting up lately, could that be the cause? We have checked and there is no friction, we can turn the flywheel just fine by hand (though we are fighting the magnets in the motors, obviously). What could cause this?

What ports are the motors plugged into?

Is the weight of the flywheel now pushing down and causing friction? Whereas before it was kind of just resting in place. Also check and make sure that none of the axles came out of the motors. And if you can take out ever other gear and make sure they are still spinning correctly. Also your gear ratio could be too high but I doubt it if you have 6 motors powering a single flywheel, but if they are all turbo motors and you have an insane gear ratio it could have an affect.

I looked at all of the motors with the gears off and found some of them were not spinning. The motor encoders seem to have blown and we are replacing them. Thanks.